--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_edger_differential_expression.py	Tue Jul 17 11:52:09 2018 -0400
@@ -0,0 +1,87 @@
+import sys, os, subprocess
+
+TRINITY_BASE_DIR = ""
+if os.environ.has_key('TRINITY_HOME'):
+    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
+elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python.
+    # 2017-09-26
+    # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
+    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
+    # I also found distutils.spawn.find_executable() which might work, but already implemented the below.
+    try:
+        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
+    except:
+        msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
+        sys.stderr.write(msg)
+        # t, v, tb = sys.exc_info()
+        # raise t, v, tb
+        # For some reason the above was giving a syntax error. 
+        # A simple raise should reraise the existing exception.
+        raise
+    else:
+        TrinityPath, err_info = pipe1.communicate()
+        # FIX - probably should be checking err_info for errors...
+        # Determine the TRINITY_BASE_DIR from output1.
+        # If TrinityPath is a link, we need to dereference the link.
+        TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
+        # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
+        # print os.path.islink(TrinityPath)
+        TrinityPath = os.path.abspath(TrinityPath)
+        # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
+        # print msg
+        # print os.path.islink(TrinityPath)
+        while os.path.islink(TrinityPath):
+            # print "That path is a link."
+            TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
+            # print "The new path is: {:s}".format(TrinityPath)
+        # Take off the last part of the path (which is the Trinity command)
+        TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
+else:
+    sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, " + \
+        "or ensure that directory is in the PATH before running.")
+    sys.exit(1)
+
+usage= "usage: " + " $counts_matrix" + " $dispersion"
+
+if len(sys.argv)<2:
+    print "Require at least two parameters, " + usage
+else:
+    print "All good- command going ahead"
+print " "
+
+def run_command(cmd):
+    # 2017-10-02
+    # Cicada Dennis put the subprocess command in a try/except statement.
+    # Errors were going undetected the way it was written previously.
+    print "Running command:\n\t" + cmd
+    try:
+        pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+        cmd_stdout, cmd_stderr = pipe.communicate()
+    except:
+        msg = "ERROR while running command:\n\t" + cmd
+        sys.stderr.write(msg)
+        raise
+    
+    sys.stdout.write(cmd_stdout)
+    ret = pipe.returncode
+    if ret:
+        print "command died: " + str(ret)
+        sys.stderr.write(cmd_stderr)
+        sys.exit(ret)
+    else:
+        # Any error output is written to stdout instead of stderr, since no error has occurred.
+        sys.stderr.write(cmd_stderr) 
+        return
+
+print ""
+
+countmatrix= "counts_matrix"
+
+cmd= "cp " + sys.argv[1] + " " + countmatrix 
+run_command(cmd)
+
+cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir"
+
+run_command(cmd)
+
+sys.exit(0)